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Retrieve Variants for Reference Identifiers and Database with GET Request

get

/ohfapi/cg/v3.3/variants/byReferenceId

This endpoint supports the retrieval of Variant Identifiers for multiple Reference Identifiers, multiple Database and single Assembly/Alignment ID.It also returns if any Invalid Reference Identifiers are passed in the Request.

Request

Supported Media Types

• application/json
• application/xml

Query Parameters

• alignmentId: integer(int64)
  Minimum Value: 0

  Assembly/Alignment ID
• database(optional): array
  Collection Format: multi

  Variant Reference Database

  • [0]: string

  {
      "name":"database",
      "in":"query",
      "description":"Variant Reference Database",
      "required":false,
      "type":"array",
      "items":{
          "type":"string"
      },
      "collectionFormat":"multi"
  }

• limit(optional): integer(int32)
  Number of rows to return
• offset(optional): integer(int32)
  Row number to start from
• referenceId: array
  Collection Format: multi

  Minimum Number of Items: 1

  Maximum Number of Items: 2147483647

  Variant Reference ID

  • [0]: string

  {
      "name":"referenceId",
      "in":"query",
      "description":"Variant Reference ID",
      "required":true,
      "type":"array",
      "items":{
          "type":"string"
      },
      "collectionFormat":"multi",
      "maxItems":2147483647,
      "minItems":1
  }

Security

• basicAuth: basic
  Type: basic

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Response

Supported Media Types

• application/json
• application/xml

200 Response

successful operation

Body ()

Root Schema : PageableDetailedCollection

Type: object

Model for paginated collections of data.

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• count(optional): integer(int64)
  Number of objects in the 'items' collection.
• hasMore(optional): boolean
  A boolean indicating if more pages are available.
• invalidAssemblies(optional): array invalidAssemblies
  List of Invalid Assemblies in request.
• invalidGeneNames(optional): array invalidGeneNames
  List of Invalid Genenames in request.
• invalidHugoNames(optional): array invalidHugoNames
  List of Invalid Hugonames in request.
• invalidReferenceIds(optional): array invalidReferenceIds
  List of Invalid Reference IDs in request.
• items(optional): array items
  A collection of paged items.
• links(optional): array links
  A collection of links containing hrefs to the current, next, and previous pages as applicable.
• resourceType(optional): string
  Identify the resource type

{
    "type":"object",
    "properties":{
        "resourceType":{
            "type":"string",
            "description":"Identify the resource type"
        },
        "items":{
            "type":"array",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of paged items.",
            "items":{
                "$ref":"#/definitions/Serializable"
            }
        },
        "count":{
            "type":"integer",
            "format":"int64",
            "description":"Number of objects in the 'items' collection."
        },
        "hasMore":{
            "type":"boolean",
            "description":"A boolean indicating if more pages are available."
        },
        "links":{
            "type":"array",
            "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
            "xml":{
                "wrapped":true
            },
            "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
            "items":{
                "type":"string"
            }
        },
        "invalidReferenceIds":{
            "type":"array",
            "description":"List of Invalid Reference IDs in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidHugoNames":{
            "type":"array",
            "description":"List of Invalid Hugonames in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidGeneNames":{
            "type":"array",
            "description":"List of Invalid Genenames in request.",
            "items":{
                "type":"string"
            }
        },
        "invalidAssemblies":{
            "type":"array",
            "description":"List of Invalid Assemblies in request.",
            "items":{
                "type":"string"
            }
        }
    },
    "description":"Model for paginated collections of data."
}

Nested Schema : invalidAssemblies

Type: array

List of Invalid Assemblies in request.

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• Array of: string

{
    "type":"array",
    "description":"List of Invalid Assemblies in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidGeneNames

Type: array

List of Invalid Genenames in request.

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• Array of: string

{
    "type":"array",
    "description":"List of Invalid Genenames in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidHugoNames

Type: array

List of Invalid Hugonames in request.

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• Array of: string

{
    "type":"array",
    "description":"List of Invalid Hugonames in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : invalidReferenceIds

Type: array

List of Invalid Reference IDs in request.

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• Array of: string

{
    "type":"array",
    "description":"List of Invalid Reference IDs in request.",
    "items":{
        "type":"string"
    }
}

Nested Schema : items

Type: array

A collection of paged items.

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• Array of: object Serializable

{
    "type":"array",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of paged items.",
    "items":{
        "$ref":"#/definitions/Serializable"
    }
}

Nested Schema : links

Type: array

A collection of links containing hrefs to the current, next, and previous pages as applicable.

Show Source

• Array of: string

{
    "type":"array",
    "example":"{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}",
    "xml":{
        "wrapped":true
    },
    "description":"A collection of links containing hrefs to the current, next, and previous pages as applicable.",
    "items":{
        "type":"string"
    }
}

Example:

{rel: 'next',href: '/patientapi/patients?limit=100&offset=300'}

Nested Schema : Serializable

Type: object

400 Response

Assembly/Alignment Id is not supplied

404 Response

Variants not found for the Reference Ids and Reference Databases supplied

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Examples

The following example submits a GET request.

API URL

http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?alignmentId=1&referenceId=rs142950474&referenceId=rs142950477&referenceId=COSM297314&referenceId=rs1&referenceId=COSM&database=dbSNP_138&database=COSMIC_COSMIC.V67&limit=2&offset=0

Example of Response Body

The following example shows the response returned in JSON format.

{
  "resourceType" : "Variants",
  "items" : [ {
    "identifier" : {
      "system" : "ODB",
      "value" : "4754980"
    }
  }, {
    "identifier" : {
      "system" : "ODB",
      "value" : "38063682"
    }
  } ],
  "count" : 2,
  "hasMore" : true,
  "links" : [ {
    "rel" : "self",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?alignmentId=1&referenceId=rs142950474&referenceId=rs142950477&referenceId=COSM297314&referenceId=rs1&referenceId=COSM&referenceId=dbSNP_138&referenceId=COSMIC_COSMIC.V67&limit=2&offset=0"
  }, {
    "rel" : "next",
    "href" : "http://localhost:7010/ohfapi/cg/v3.3/variants/byReferenceId?alignmentId=1&database=dbSNP_138&database=COSMIC_COSMIC.V67&offset=2&limit=2&referenceId=rs142950474&referenceId=rs142950477&referenceId=COSM297314&referenceId=rs1&referenceId=COSM"
  } ],
  "invalidReferenceIds" : [ "rs1", "COSM" ]
}

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